The Hammers cult hero was expected to leave the Premier League side and complete a move to Spain on Thursday night.
However, Real Betis CEO Ramon Alarcon said they while the LaLiga club had submitted the relevant documents on time, West Ham had a technical fault.
He then claimed that the club were working to rectify the issue after missing the deadline and they now look set to welcome their man.
According to talkSPORT football reporter Ben Jacobs, FIFA have cleared the move for Fornals to join Real Betis in a deal worth around £6.8million.
The 27-year-old Spaniard joined West Ham from Villarreal in 2019 and made 203 appearances across all competitions, scoring 23 goals.
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His strike against AZ Alkmaar in the Europa Conference League last season helped guide them to the final, which they won to lift their first trophy since 1980.
Fornals has already featured in 23 matches this season for the Hammers but is yet to score or assist in the current campaign.
He has also made just four Premier League starts and is now in line for a return to the Spanish top-flight.
The attacking midfielder already has 129 appearances to his name in La Liga following spells at Malaga and Villarreal.
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Fornals joins a Real Betis side who sit 7th in the table and he may be one of two upcoming departures from West Ham.
Said Benrahma is now on course to complete a move to French side Lyon after his £15million switch collapsed on Deadline Day.
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The winger underwent a medical with the Ligue 1 outfit but the two clubs could not agree a deal, with Lyon said to be furious after they registered all the relevant details on FIFA's Transfer Management System [TMS] by 10.30pm on Thursday night.
They accused West Ham of mismanaging the paperwork and took the case to FIFA, who have given the green light for the transfer to be completed.